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Ambiguity Consensus Maker

Purpose: Make a consensus of IUPAC ambiguity codes for an alignment, or for blocks of sequences in an alignment. This tool works only for nucleotide alignments.

Usage: Browse or paste your alignment, choose options, and click "Run". You can specify the character presence percentage, which is the minimum representation required for a character to be considered in computing the consensus for that column. For example, a column containing 99 "A" and 1 "G" will be scored as "R" if the percentage is 0, but will be scored as "A" if the character presence is set at 1% or greater. In the latter case, the G would be ignored since it does not exceed 1% of the total. Note that all characters other than ACGTU are ignored. For details, see Ambiguity Consensus Maker Explanation.

Input
Paste your alignment
Or browse for your file
Squeeze gaps in input  Yes  No      Gap character
Output Options
Do consensus for each block  Yes  No
Minimum number of sequences for consensus
Show both consensus + alignment  Yes  No
Show number of sequences in consensus  Yes  No
Output format  Pretty  Output aligned  Like input
Consensus-making Options
Character presence percentage

last modified: Thu Mar 8 11:29 2012


Questions or comments? Contact us at seq-info@lanl.gov.

 
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